You have a strange setup. First off, I have never worked with MicroTik, so if they do something weird, I can't help with that. My experience with QinQ is with a telecom company providing a connection to a customer over fibre. Since fibre has so much bandwidth, it's usually split before reaching the customer. The first method it to use different wavelengths, with an optical filter located near the customer. Then QinQ (C tag)¹ is used to separate different customers. Depending on the connection, the 2nd VLAN (S tag) can be used to further subdivide the bandwidth or passed on to the customer. In the jobs I worked on, there was a media converter to convert between fibre and Ethernet and used the 2nd VLAN to connect it to a Cisco router, which then provided IP over Ethernet to the customer. So, I'm surprised you'd have QinQ on the WAN.
As for MTU that's determined by whatever the interface is configured for. As I mentioned earlier, VLAN tags do not affect that, since they're ahead of the Ethertype field. On my own network, while I can set the MTU on the native LAN, I can't on the VLAN. It just follows whatever the native LAN provides. I also checked adding a VLAN and found I can only add them to an interface, not on top of another VLAN. You found similar with the bridge. It's just not something pfSense can do, as far as I can tell.
As for connecting the VLANs between sites, that's normally done by routing the subnets, through a VPN if necessary. Do you actually have Ethernet between sites? Or just IP? If Ethernet, do you have something like MPLS to carry it?
Is there anyone else here who knows MicroTik?
C tag = carrier level VLAN S tag = subscriber level VLAN.